The NDEx Team is happy to announce that NDEx v2.3.1 is now available to use on the Public NDEx Server! A downloadable installation bundle is also available on our FTP Server for sites running their own NDEx instances. New features in NDEx v2.3.1 simplify the user experience and support publication and dissemination of ...
The November 1st issue of Cancer Research contains a special section (online only) focused on computer resources supporting cancer research. The purpose of this collection is to highlight freely available computer tools and resources that non-bioinformaticists can introduce in their workflows. Each resource...
Summer is finally here and so is the second NDEx update planned for 2017! NDEx 2.1 provides several new features to support collaboration and publication of networks. Network Sets allow users to create collections of networks while the Share URL feature makes sharing networks as simple as sharing a document...
The first quarter of 2017 is over and the NDEx Team is ready to roll out the Q1 Update! The Q1 Update restores all of the features that had been temporarily disabled in the NDEx 2.0 release last December: bulk actions and network property editing functions are now available again while the Advanced Query function allows users to query a network...
Less than 2 weeks have passed since the release of the NDEx 2.0 Preview Server and thanks to your support, we are proud to announce that NDEx 2.0 is READY for prime time… NDEx 2.0 is now live on our Public Server at www.ndexbio.org. Differently from previous releases, NDEx 2.0 is only available on our Public...
We promised we were going to do it… and the NDEx Team always keeps its word! NDEx 2.0 is getting ready for prime time and we have decided to give everyone the opportunity to preview and test it before is officially released on the NDEx Public Server. The NDEx 2.0 Preview Server is a clone of...
The NDEx Project is involved in a collaboration with the Peter Sorger's lab as part of two DARPA-funded programs: BIG MECHANISM and COMMUNICATING WITH COMPUTERS. One output of these collaborations is The RAS Machine network, available on the NDEx Public Server and automatically updated daily. The RAS Machine integrates diverse inputs ranging from BEL curated documents, BioPAX...
Thanks everyone for your support…@NDExProject has 100 followers!!! Looking forward to see it growing even more… pic.twitter.com/Vn5lLnxuy1 — The NDEx Project (@NDExProject) June 1, 2016
The NDEx Team is always striving to improve and simplify our end user experience… after receiving their valuable feedback, we focused on enhancing the NDEx search feature. First of all, searching for biological networks in NDEx is now easier thanks to the addition of a "Browse" button that will let users explore the entire server's content. We also...
In an effort to provide usable data in the form of biological networks, the NDEx Project has developed a content plan that aims to provide access to a vast array of drug/compound data from several different databases. To date, the NDEx Public Server offers a selection of networks from DrugBank, Therapeutic Target Database (TTD) and...
"After 8 months of hard work, we have finally reached the finish line… We are proud to announce that NDEx v1.3 is officially released! We want to thank all our users and collaborators for providing valuable feedback during this long effort of development and testing." And we look forward to your continued support… Please keep...
Howdy NDEx enthusiasts! In the February newsletter we announce our participation as exhibitors at ISMB 2016, feature an article about therapeutic epigenetics and remind you that the deadline for the Open Science Prize Challenge is approaching fast! >> READ OUR NEWSLETTER HERE
In living organisms, genes encode proteins and proteins form complexes, resulting in an intricate network of interactions that is responsible for orchestrating all biological cellular processes. The human genome has around 20,000 protein-coding genes and only a small fraction of these proteins has been characterized at the functional level… For this reason, a new project led...
Happy New Year from the NDEx Team! In the first newsletter of 2016 we describe a new knowledge base for naturally occurring venoms, feature an article about bioinformatic resource funding and remind you to come check us out at the XXVI Plant and Animal Genome (PAG) conference in sunny (not so much lately) San Diego!...
The December newsletter is all about the NDEx v1.3 Release candidate! Several new features and architectural changes characterize the new NDEx v1.3… Learn more about the CX interchange format and the future of the Cytoscape Cyberinfrastructure. >> READ OUR NEWSLETTER HERE
Melanoma is one of the most aggressive human cancers. Similar to many other cancers, melanoma is initiated by activation of oncogenes or inactivation of tumor suppressor genes. However, there is no database available yet focusing on genes involved in melanoma causation. In this view, Dr. Zhang and collaborators have manually curated a vast body of literature and created...
This month we focus on the NDEx Publication now available on Cell Systems, we announce a new collaboration that will bring plant networks to NDEx and feature the International Mouse Phenotyping Consortium (IMPC). >> READ OUR NEWSLETTER HERE We want to hear your voice… Give us your feedback and help us improve NDEx! Connect with us...
The NDEx Team is proud to announce that the first NDEx paper has been published in the October 28 issue of "Cell Systems". Two full years of work, meetings, testing and constant interaction with users and stakeholders have helped us reach this important milestone… Thanks everyone for your hard work! And we are sure you...
Technology advancements provide access to huge amounts of data and today's scientists biggest obstacle is to analyze these data sets in order to make meaningful data-driven decisions. Most importantly, the analytic tools need to be simple enough to be used by biologists that often lack advanced bioinformatic skills; tasks such as annotating a gene list or performing ID conversion...
The NDEx Project is happy to announce that the October Newsletter is out! In this month's news from the NDEx Team we offer you the opportunity to transform your datasets into novel networks, we feature a nifty tool for literature and web research and link to an interesting article on mining cell line names in scientific...
Rb, p53, PTEN… Many genes are known for their ability to keep cancer under control thus acting as tumor suppressors. But what if a tumor suppressor gene could also act as an oncogene and stimulate cancer growth rather than inhibiting it? Are we looking at a new class of "double-cross" genetic elements? A new article...
The NDEx Project is glad to announce that the September newsletter is out!!! This month we show some amazing performance improvements that you can expect in our next release, NDEx v1.3, later in Q1 2016. We also feature an interesting research article by Bikel and collaborators focused on the human microbiome. Finally, we present an...
Elsevier and Cytoscape have joined forces to create a networks viewer that allows authors to publish fully interactive network diagrams as part of their articles on ScienceDirect.com. Detailed instructions for authors and links to publications that use this new feature are available here. As of phase 1, the interactive viewer allows some basic actions like moving nodes and...
The NDEx Team is proud to announce that NDEx v1.2 is now available on our Test and Public servers as well as on our FTP site for all who prefer to install and run their own, private NDEx server instance. The NDEx v1.2 release has many new features, changes in the user interface and improvements to boost stability as well as functionality; therefore, we strongly recommend a careful review of our documentation for...
Howdy!!! The NDEx Team would like to share some news and hopes you'll find it interesting! Follow us on LinkedIn or visit our website to stay informed on new project features, releases and other interesting content and subscribe to our YouTube channel! Questions? Comments? We ‘d be happy to hear from you! NDEx v1.2 Release Candidate...
Tribe is a collaborative platform that allows mining of big data across bioinformatics systems. Here at the NDEx Project, we are excited to find a system with a similar philosophy and complementary content. Tribe has features that make it an interesting resource for both biology and bioinformatics researchers and we look forward to evaluating it...
Howdy !!! The NDEx Team would like to share some news and hopes you'll find it interesting! Follow us on LinkedIn, subscribe to our Youtube channel and visit our website to stay informed on new project features, releases and other interesting content! Questions? Comments? We ‘d be happy to hear from you! The new "NDEx...
Hello Past & Future Hackers!!! TSRI is hosting a BD2K / "Network of BioThings" hackathon May 7-9th 2015. The purpose of this hackathon is to bring together experts in their respective fields to collectively work on solving challenges related to biomedical big data. This hackathon will feature networking and mentoring with leading researchers and experts,...
The NDEx Team keeps growing… Vladimir Rynkov, our new software engineer, will join efforts with Jing Chen to develop/manage the NDEx back-end, ensure that our servers run smooth and guarantee a solid performance. Check out out team members page for more information about Vladimir's background and experience!
It's that time of the year… and the NDEx Project is ready to spring forward to provide new features and content to the scientific community! On March 6th, 2015 we updated the NDEx Public Server to the latest version (1.2 Alpha), bringing to you enhanced stability and performance, several UI changes for an improved user experience...
The NDEx Team is right on schedule for the release of NDEx v1.2 in Q2 2015 and has decided to make an NDEx v1.2 alpha version available for you to evaluate! Explore and start enjoying some of the great improvements you will see in the final NDEx v1.2. Besides improved server stability, scalability and performance,...
In an effort to provide even more resources to our scientific community, the NDEx Project now provides links to publications focused on network biology as well as relevant conferences coming up in 2015! The list of Network Biology publications is maintained on Tumblr by the Network Biology Group. These useful resources can be conveniently accessed from the home page of...
The NDEx Project aims to become a main hub for storing, sharing and publishing biological network data and a very important part of our efforts is focused on providing interesting, valuable and re-usable content to enable interaction and collaboration within the scientific community worldwide. We recently updated the NDEx database to include the latest "Extended...
The NDEx Project is happy to announce that his Lead Software Engineer, Dr. Jing Chen, has officially joined the NDEx Development Team on a full time basis! Dr. Chen has many years of experience in software development focused on the integration and management of life science data. Prior to joining the NDEx Team, Dr. Chen worked at...
The NDEx Team has announced that NDEx v1.1 will be officially released in January 2015. New features include but are not limited to: Lucene indexing for network searches and queries, an improved web UI and a brand new, user oriented Informational Website with tutorials, technical resources, news and more! The release of NDEx v1.1 will...
The Cytoscape team worked hard to bring v3.2 right at your fingertips !!! Faster startup, experimental support for Java 8, interactive web visualization, chart editor, gradient effects and a lot more… Download Cytoscape 3.2 and discover all the new features available!